Cell splicing factor controls macrophage defense against tuberculosis

Tuberculosis develops when the balance between the bacterium Mycobacterium tuberculosis (Mtb) and the body’s immune defenses is disturbed. Macrophages, a type of immune cell, are a first line of defense that must respond precisely to keep this balance. One way cells adjust their responses is through alternative splicing, the process that allows a single gene to produce multiple mRNA messages and different protein variants. KL Patrick and colleagues set out to understand how alternative splicing shapes the early macrophage reaction to Mtb. They infected bone marrow-derived murine macrophages with Mtb and used RNA-sequencing together with splicing-aware computational pipelines to measure changes in how genes were spliced after infection. Remarkably, about 5% of expressed macrophage genes showed one or more splicing changes eight hours after infection. That scale of change highlights alternative splicing as a major regulatory mechanism in the macrophage response to Mtb, suggesting that shifting which mRNA variants are made can quickly tune immune functions during infection.

To find what controls those splicing changes, the team searched for RNA binding proteins that reshape the macrophage transcriptome during infection. They identified the splicing factor heterogeneous nuclear ribonucleoprotein A2B1 (hnRNPA2B1) as a key player. Using their RNA-sequencing data and computational analyses, they found that hnRNPA2B1 promotes the early induction of inflammatory genes while reducing the expression of several type I interferon-stimulated genes in response to Mtb. hnRNPA2B1 also controlled alternative splicing of many individual genes, including Irgm1, which encodes a critical immunity-related GTPase. The researchers showed that the balance between Irgm1-long and Irgm1-short isoforms shifts with different inflammatory signals. Importantly, macrophages engineered to overexpress Irgm1-short were impaired: they showed defective autophagosomal targeting, altered lysosomal homeostasis, and a reduced ability to restrict Mtb replication. Taken together, these results point to hnRNPA2B1 as a previously unrecognized restriction factor that shapes cell-intrinsic antimycobacterial defenses through alternative splicing.

These findings place alternative splicing at the center of how macrophages fine-tune their response to Mtb and identify hnRNPA2B1 as a crucial regulator of that tuning. By controlling whether genes like Irgm1 produce long or short isoforms, hnRNPA2B1 influences processes such as autophagy and lysosomal maintenance that are directly involved in containing bacterial replication. The demonstration that an excess of Irgm1-short undermines autophagosomal targeting and lysosomal function provides a clear example of how splicing decisions can change cell behavior in ways that matter for infection control. For researchers and clinicians, this work suggests new directions: studying splicing factors and isoform balances could reveal why some macrophages fail to contain Mtb and may point to molecular levers that could be adjusted to improve host defenses. While the study focused on early changes in cultured murine macrophages, its identification of hnRNPA2B1 and Irgm1 isoform balance as central nodes provides a focused framework for future investigations into tuberculosis immunity.